W.J.
Have you considered giving her a slow wean off breastmilk to whole milk. DO an overpump so you have stock. For about 3-4 days, give her 75% breastmilk and 25% dairy. Then if she is doing ok, go 50-50. Then if she is tolerating that go 25% breast milk and then 75% dairy. Eventually you will get her off the breast. A good wean unless the child initiates it takes about a month.
The other thing you might consider is that this soft stool is a stress related response because she desires your closeness with a latch but now she is stuck with a cup of something to drink and is not latching so that stress of change is leading her to have soft stools.
Good luck!